Biology Research Paper
In terms of causing some type of vascular spasm so at any rate they won’t be involved in aiding a healing process, so the prostaglandins and leukotrines contribute to pain, swelling & the healing process itself , inflamation. Amino acids, talk about peptide bonds. Proteins basically are made up of carbohydrates, hydrogen, oxygen and now we add nitrogen. In terms of carbohydrates (they make up 2% - 3% of our total body weight) and are basically made up of nothing more than carbon, hydrogen, & oxygen. Lipids make up 18 - 25% of our total body weight (made up of carbon, hydrogen & oxygen) that’s why they’re so easily interchangeable, in terms of breaking up bonds and utilizing those bonds for energy, so that I can have utilized those lipidous constituents and be able to convert them into energy molecules. Makes it more viable. If I look at proteins on the other hand, proteins have carbon, hydrogen & oxygen, but now we add nitrogen to the mix. Adults basically have 12-18% in our total body weight. Proteins are structual components within the body.
The rest is water. When we look at proteins, they are made up of amino acids. The amino acids are the building blocks of all proteins. There are 20 different types of amino acids. We’ll see 7 different types listed on our outline. The key here is that all amino acids, have a nitrogenous base as you can see on the outline, an NH2 group affiliated with carbons and hydrogens, and oxygens. The nitrogenous group that’s where nitrogen comes from, you have the carbons, hydrogens & oxygens, now you have an R group. When you see the letter R, you can replaced by any type of constituent, any other type of atom, or molecule for that matter. You replace it with hydrogen, it becomes glycine. You replace it with a methyl group a CH3 or a CH4 or a CH2OH, they don’t really mean that much to us, but we do have 20 types of amino acid. On the (c?g) on our paper what would be the R group? The whole chain, in this particular group, not only do you have your nitrogenous group and you have your usual carbon skeleton, but that R group is made up of 3 methyl groups, another nitrogenous group a carbon with 3 nitrogenous groups, that’s argenine. Tryptophan where it’s all blocked out, the shadow part is usually our base of the amino acid and the R group is the rest of it. The protein, depending on the protein will have a combination of thousands of these amino acids, depending on sequence. Can have a glycine glycine, a serine argenine, argenine argenine, serine glycine, a phenolalonine. It is amazing that the human body can use this as a building block and rearrange them in all different kinds of sequences and build what we are and what we look like. Amazing. We join amino acids by dehydration synthesis process.
Remember any kind of organic compound, whether its a protein, lipid, carbohydrate or a nucleic acid, no matter what it is, it always, always, always will be joined by dehydration synthesis. Always going to be split by hydrolosis, we’re breaking it with water. On outline it says peptide bonds, just the name of the bond between two amino acids. Amino acids are also know as peptides, so they’ll be referred to sometimes as peptides rather than amino acids to form a peptide bond. When I then join two amino acids together I have a di-peptide, three a tri-peptide and so on until I get to many, many, many amino acids and then I have a polypeptide. So that when I look at the sequence of a protein which is normally a polypeptide basically all I have in terms of sequence is that I have a primary structure of a protein this is the linear sequence of amino acids, which tells me what the sequence of amino acids in that particular chain will be. So if you look at a polypeptide for example, here you have a polypeptide made up of 6 amino acids that would be your linear sequence. That would be your linear structure or primary structure. The secondary structure is nothing more than the coiling of protein is not simply a series of amino acids in a linear sequence. Linear sequence is what they figure out when they dissect the protein. The proteins are usually found in a three dimensional shape and so consequently what happens is that when we look at them they are usually arranged into some kind of coil, which is a helix. Wasseman Frick also dated the structure of proteins and that of DNA and found the DNA to be a double helix. In terms of proteins, they normally form some kind of a coiled sequence that is usually in a helical shape. It’s also found to be in a pleated shape. So there are two types of shapes, a coiled or helix and a pleat. This is what you find in proteins, they are sequenced in a coil, pleat or linear, it looks like circuitry but its not. What happens is when I look at the tertiary structure of a protein basically what the tertiary structure of a protein implies is how it falls on itself. How it literally falls on itself into the three dimensional structure that it is. Basically look at it this way, if I take a telephone cord, it’s a coil, if I pull on it appears to be almost linear but has pleats, but if I stretch it all the way I get rid of the bumps and it is basically linear, if I release it, it returns back to the coil. In terms of envisioning what a protein looks like basically is this; is my linear sequence just tells me that what I’ve done is taken that coil or that pleat and stretched it out so I can find out what those amino acids are. When I let it go a little bit I can see that it can take on different shapes but the final shape is the coiled telephone cord. Now what happens three dimensionally, nothing in the body is just in a straight line regardless whether it is a coil or a pleat or whatever, because of the three dimensionallity of everything in our bodies. So what happens is, if I take that telephone cord and drop it, whatever shape it takes, it is all discombobulated a mass of coils. The mass of coils is the three dimensional shape, that your tertiary structure. We can basically take all these different shapes and stretch them out and sequence what we have in this particular protein. Then your gonna see quarinary shape. A quarinary structure is multiple polypeptide chains. That refers to different types of molecules within the body, as an example you take something like hemoglobin. Hemoglobin is made up of four polypeptide chains that are joined together called alpha chains and beta chains, basically we don’t always have single chains, we sometimes have multiple polypeptide chains that will combine to form gigantic molecules and this is probably the reason why when you analyse what happens in the human body, they always told us that we need protein, but high protein diets can be dangerous. Why? Because proteins are gigantic molecules, they’re usually hundreds of thousands amino acids. They are water soluable which means they won’t get through the cells very easily. If they can’t get thru the cells easily, they are going to need mediators to help them get through. If they force themselves through the cell (think about it in terms of the kidneys) an athlete who is on a very high protein diet as an example, they will get blood in the urine, because the kidney is made up of millions and millions of tiny, tiny, microscopic filtering factors, one cell layer thick, known as nephrons. Because they’re filters we need osmosis, were not going to filter through ten layers of cells. Could you exchange gases in your lungs if they were ten cell layers thick? It must be like a sieve, that’s what a kidney does, like a sieve it filters out the bad stuff (or like water from pasta) because these proteins are so gigantic, no matter how selective those filters are they can’t filter through very well so they keep pushing through until finally they rip or tear the cellular sieve, that’s when you get blood in the urine. After the injury you develop scar tissue in the kidney which is a super filter, got about 15 million of these nephrons per kidney, but if you develop pockets of scar tissue one can’t filter through all of the collecting tubles that then filter into the ureters to the bladder. So when you look at a kidney itself you have a passage way thats going to filter little lobules in each kidneys and within the lobules are the nephrons. Due to scar tissue the kidney will eventually become ineffective. That then brings us to the aspect of structural vs functional proteins. Plasma proteins are extremely important proteins in the body, because plasma proteins will contribute to maintaining water balance in the body. Although there are many, many plasma proteins the most important plasma protein is albumin. Albumin is a functional protein and is the smallest plasma protein and it’s purpose is to produce osmotic pressure. Most plasma proteins are produced by the liver. Osmotic pressure implies we are using water so osmotic pressure is nothing more than a pressure gradient that will be produced to prevent the movement of water into or out of a particular area when we have solutes that are in that area. If I have a semi-permeable membrane (selective and allows different constituents to move in and out). water will go both ways.
The rest is water. When we look at proteins, they are made up of amino acids. The amino acids are the building blocks of all proteins. There are 20 different types of amino acids. We’ll see 7 different types listed on our outline. The key here is that all amino acids, have a nitrogenous base as you can see on the outline, an NH2 group affiliated with carbons and hydrogens, and oxygens. The nitrogenous group that’s where nitrogen comes from, you have the carbons, hydrogens & oxygens, now you have an R group. When you see the letter R, you can replaced by any type of constituent, any other type of atom, or molecule for that matter. You replace it with hydrogen, it becomes glycine. You replace it with a methyl group a CH3 or a CH4 or a CH2OH, they don’t really mean that much to us, but we do have 20 types of amino acid. On the (c?g) on our paper what would be the R group? The whole chain, in this particular group, not only do you have your nitrogenous group and you have your usual carbon skeleton, but that R group is made up of 3 methyl groups, another nitrogenous group a carbon with 3 nitrogenous groups, that’s argenine. Tryptophan where it’s all blocked out, the shadow part is usually our base of the amino acid and the R group is the rest of it. The protein, depending on the protein will have a combination of thousands of these amino acids, depending on sequence. Can have a glycine glycine, a serine argenine, argenine argenine, serine glycine, a phenolalonine. It is amazing that the human body can use this as a building block and rearrange them in all different kinds of sequences and build what we are and what we look like. Amazing. We join amino acids by dehydration synthesis process.
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Remember any kind of organic compound, whether its a protein, lipid, carbohydrate or a nucleic acid, no matter what it is, it always, always, always will be joined by dehydration synthesis. Always going to be split by hydrolosis, we’re breaking it with water. On outline it says peptide bonds, just the name of the bond between two amino acids. Amino acids are also know as peptides, so they’ll be referred to sometimes as peptides rather than amino acids to form a peptide bond. When I then join two amino acids together I have a di-peptide, three a tri-peptide and so on until I get to many, many, many amino acids and then I have a polypeptide. So that when I look at the sequence of a protein which is normally a polypeptide basically all I have in terms of sequence is that I have a primary structure of a protein this is the linear sequence of amino acids, which tells me what the sequence of amino acids in that particular chain will be. So if you look at a polypeptide for example, here you have a polypeptide made up of 6 amino acids that would be your linear sequence. That would be your linear structure or primary structure. The secondary structure is nothing more than the coiling of protein is not simply a series of amino acids in a linear sequence. Linear sequence is what they figure out when they dissect the protein. The proteins are usually found in a three dimensional shape and so consequently what happens is that when we look at them they are usually arranged into some kind of coil, which is a helix. Wasseman Frick also dated the structure of proteins and that of DNA and found the DNA to be a double helix. In terms of proteins, they normally form some kind of a coiled sequence that is usually in a helical shape. It’s also found to be in a pleated shape. So there are two types of shapes, a coiled or helix and a pleat. This is what you find in proteins, they are sequenced in a coil, pleat or linear, it looks like circuitry but its not. What happens is when I look at the tertiary structure of a protein basically what the tertiary structure of a protein implies is how it falls on itself. How it literally falls on itself into the three dimensional structure that it is. Basically look at it this way, if I take a telephone cord, it’s a coil, if I pull on it appears to be almost linear but has pleats, but if I stretch it all the way I get rid of the bumps and it is basically linear, if I release it, it returns back to the coil. In terms of envisioning what a protein looks like basically is this; is my linear sequence just tells me that what I’ve done is taken that coil or that pleat and stretched it out so I can find out what those amino acids are. When I let it go a little bit I can see that it can take on different shapes but the final shape is the coiled telephone cord. Now what happens three dimensionally, nothing in the body is just in a straight line regardless whether it is a coil or a pleat or whatever, because of the three dimensionallity of everything in our bodies. So what happens is, if I take that telephone cord and drop it, whatever shape it takes, it is all discombobulated a mass of coils. The mass of coils is the three dimensional shape, that your tertiary structure. We can basically take all these different shapes and stretch them out and sequence what we have in this particular protein. Then your gonna see quarinary shape. A quarinary structure is multiple polypeptide chains. That refers to different types of molecules within the body, as an example you take something like hemoglobin. Hemoglobin is made up of four polypeptide chains that are joined together called alpha chains and beta chains, basically we don’t always have single chains, we sometimes have multiple polypeptide chains that will combine to form gigantic molecules and this is probably the reason why when you analyse what happens in the human body, they always told us that we need protein, but high protein diets can be dangerous. Why? Because proteins are gigantic molecules, they’re usually hundreds of thousands amino acids. They are water soluable which means they won’t get through the cells very easily. If they can’t get thru the cells easily, they are going to need mediators to help them get through. If they force themselves through the cell (think about it in terms of the kidneys) an athlete who is on a very high protein diet as an example, they will get blood in the urine, because the kidney is made up of millions and millions of tiny, tiny, microscopic filtering factors, one cell layer thick, known as nephrons. Because they’re filters we need osmosis, were not going to filter through ten layers of cells. Could you exchange gases in your lungs if they were ten cell layers thick? It must be like a sieve, that’s what a kidney does, like a sieve it filters out the bad stuff (or like water from pasta) because these proteins are so gigantic, no matter how selective those filters are they can’t filter through very well so they keep pushing through until finally they rip or tear the cellular sieve, that’s when you get blood in the urine. After the injury you develop scar tissue in the kidney which is a super filter, got about 15 million of these nephrons per kidney, but if you develop pockets of scar tissue one can’t filter through all of the collecting tubles that then filter into the ureters to the bladder. So when you look at a kidney itself you have a passage way thats going to filter little lobules in each kidneys and within the lobules are the nephrons. Due to scar tissue the kidney will eventually become ineffective. That then brings us to the aspect of structural vs functional proteins. Plasma proteins are extremely important proteins in the body, because plasma proteins will contribute to maintaining water balance in the body. Although there are many, many plasma proteins the most important plasma protein is albumin. Albumin is a functional protein and is the smallest plasma protein and it’s purpose is to produce osmotic pressure. Most plasma proteins are produced by the liver. Osmotic pressure implies we are using water so osmotic pressure is nothing more than a pressure gradient that will be produced to prevent the movement of water into or out of a particular area when we have solutes that are in that area. If I have a semi-permeable membrane (selective and allows different constituents to move in and out). water will go both ways.
If I have a container water will go nowhere.
If I have a container of particulate water the water will go to the left because the container on the right has more water, because the water on the left has been displaced by particles. Water will always go from a an area of high concentration to an area of low concentration. Once I have a semi-permeable membrane, the particles are blocked from movement, it allows filtration of the certain particles to move, this is how dialysis works. Because in dialysis we have failed kidneys, so we have to filter everything through, we are filtering those particles, so we’re keeping particular particles in depending on size. Osmotic pressure - water pressure, so all you want to do is move water. So the whole purpose of plasma proteins is maintaining water balance in the body regardless of what that body is. Now suppose I have the water will go to the right because I have displaced water on this side with more particles. This would be a hyper tonic solution. Hyper tonic means I have more particles than water. Hypo tonic means I have less particles than water. Have vascular tree supposing I have an injury and I have blood loss. With the loss of blood (an even exchange between artery and interstitial fluid between the vascular tree and the fluid outside, we are maintaining water pressure constantly. Means I will have the same amount of particles on the inside as the outside. So water is flowing in and out. Lose a tremendous amount of blood, also loose water and particulate matter, now have a total imbalance. The body senses this imbalance and immediately tries to rebalance by sending leutin?, to start filling situation with particles so that we can maintain the water balance within the cardiovascular tree.
Constantally maintaining water pressure, between blood and tissues. Antibodies, another functional protein, called immunoglobulins. Antibodies are produced by the liver and certain plasma cells (which are nothing more than white blood cells or lymphocytes). These white blood cells produce these immunoglobulins (immuno meaning immunological, globulins are our proteins) and basically they produce antibodies. Antibodies attack antigen (any thing foreign to the body). Mainly the lymphocytes attack viruses and some bacteria. Hemoglobin says lipoproteins in this situation as well. Lipoproteins, talked about HDL vs. LDL. When I talk about HDL, I want that high density lipoprotein water solueable to move those fats to either storage areas or adipose tissue or transport them to where they can be digested and consequently eliminated. Hemoglobin is obviously the hem portion which is the iron portion and the globin (part of red blood cell) which is the protein portion. Purpose of hemoglobin is to transport oxygen and/or carbon dioxide, depending on which direction it is travelling. We have thrombinfibrinogen and fibron, we have a situation here where we have functional proteins which will eventually give way to a structural proteinaceous end product. I have functional proteins, thrombin and a fibrinogen and basically these are going to be involved in blood clotting. Thrombin and fibrinogen basically the functional proteins that are going to be involved in a structural remodeling by virtue of fibrous proteinaceous strands known as fibrogin, that is the clot itself. Blood pouring out, apply pressure stop bleeding it starts to develop a film, it you touch it, it will be stringy and sticky, and then starts to bleed again. That is the structural fibrin that is sort of covering that cut, until we start to form a scab. The scab is formed by virtue of the fact that I’ve formed this fiberous mesh work that is infiltrated by all the other white blood cells, now I get that pusy like exudate. Pus is nothing more than white blood cells and blood serum. Develops because white blood cells are like little pac men, they eat all the debris and engorge themselves until they burst.
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